An internal combustion engine combusts a mixture of air and fuel within cylinders to generate drive torque at a crankshaft. Scavenging refers to an operating mode of the engine where a specific overlap of the cylinder intake and exhaust valves being open is commanded such that cylinder delta pressure between the intake and exhaust forces the air charge to blow through the cylinder and exit via the exhaust valve. Scavenging operation potentially increases engine performance at certain operating conditions, such as low engine speeds when exhaust energy available for a turbocharger is low. For example, scavenging affects exhaust gas dynamics, which in turn improves boost response at the turbocharger. Engine flow control valves (throttle valve, wastegate valve, etc.) are typically controlled based on related air/exhaust flow set points. Scavenging operation causes the volumetric efficiency (VE) of the engine to change, which potentially causes these engine flow set points to fluctuate. As a result, the flow control valves fight against each other, which decreases transient response of the engine. Accordingly, while such engine control systems work well for their intended purpose, there remains a need for improvement in the relevant art.